; RUN CONTROL PARAMETERS =
define =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.010
nsteps = 1000000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = System
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 1000
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 0
xtc_precision = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps = Protein
; Selection of energy groups =
energygrps = System
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = simple
; Periodic boundary conditions: xyz or none =
pbc = no
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = berendsen
; Groups to couple separately =
tc-grps = System
; Time constant (ps) and reference temperature (K) =
tau_t = 1
ref_t = 323
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 300
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 90